[R] Computing sums of the columns of an array

[Liaw, Andy]

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Uwe Ligges
> Sent: Friday, August 05, 2005 12:44 PM
> To: Duncan Murdoch
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] Computing sums of the columns of an array
> 
> 
> Duncan Murdoch wrote:
> 
> > On 8/5/2005 12:16 PM, Martin C. Martin wrote:
> > 
> >>Hi,
> >>
> >>I have a 5x731 array A, and I want to compute the sums of 
> the columns.  
> >>Currently I do:
> >>
> >>apply(A, 2, sum)
> >>
> >>But it turns out, this is slow: 70% of my CPU time is spent 
> here, even 
> >>though there are many complicated steps in my computation.
> >>
> >>Is there a faster way?
> > 
> > 
> > You'd probably do better with matrix multiplication:
> > 
> > rep(1, nrow(A)) %*% A
> 
> 
> No, better use colSums(), which has been optimized for this purpose:
> 
>   A <- matrix(seq(1, 10000000), ncol=10000)
>   system.time(colSums(A))
>   # ~ 0.1 sec.
>   system.time(rep(1, nrow(A)) %*% A)
>   # ~ 0.5 sec.

With the dimension that Martin stated, I don't see much difference:

> A <- matrix(runif(5 * 731), 5)
> system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)
[1] 5.28 0.13 5.46   NA   NA
> system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)
[1] 1.99 0.20 2.22   NA   NA
> system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)
[1] 1.97 0.25 2.28   NA   NA
> system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE)
[1] 1.90 0.20 2.16   NA   NA
> system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)
[1] 1.53 0.22 1.75   NA   NA
> system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)
[1] 1.53 0.19 1.72   NA   NA
> system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)
[1] 1.51 0.19 1.70   NA   NA
> system.time(replicate(1e4, colSums(A)), gcFirst=TRUE)
[1] 1.49 0.25 1.79   NA   NA

However, I don't understand why the first try took so much longer.

Andy 

 
> Uwe Ligges
> 
> 
> 
> > Duncan Murdoch
> > 
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